


Soldier

by Elanshaw



Category: Stargate Atlantis
Genre: Angst, Gen, Hurt/Comfort, Psychological Torture, Psychological Trauma
Language: English
Status: Completed
Published: 2020-06-08
Updated: 2020-06-13
Packaged: 2021-03-03 21:02:13
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 10
Words: 19,379
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/24611965
Author URL: https://archiveofourown.org/users/Elanshaw/pseuds/Elanshaw
Summary: When John is taken, the team wonders if the man they know and love will ever return to them.
Kudos: 19





	1. Chapter 1

**Author's Note:**

> This is my very first fanfic I ever wrote, so I wanted this to be one of the ones I transferred over from FFN. I hope you enjoy it. :) / Beckett is in this one instead of Keller.

Ronon was already twirling his Bantos rods when John walked in.

"You're late."

John smirked, pulling out his rods from his bag. "Had to see a man about a horse."

"A what?"

"Never mind." laughed John. He started circling the large man, rods twirling.

"So Buddy, you know I've been practicing with Teyla and I think I'm getting…"

Ronon swung his leg low to the ground knocking John to his knees then struck him across the chest with one rod and the side of the head with the other.

"Oof..!" John fell to the ground.

"You were saying?" smiled Ronon, he held out a hand and pulled him to his feet. John staggered slightly a bruise starting to form near his temple.

Ronon frowned, "You okay?

John waved him off with a smirk while rubbing his head and chest. "Yeah, yeah." He blinked rapidly a few times. "But can you give a guy a little warning next time?"

Grinning, Ronon pat him on the back, "You need to go see Beckett."

"Chewie, I got a hard head remember? I'm fine!" John took a step and swayed.

"Humor me." Ronon spun him around and with a hand on his shoulder led him to the door.

Sighing, John allowed himself to be led.

As they neared the infirmary, John's comm buzzed.

"Sheppard."

_“John, its Teyla. Mr. Woolsey would like to see us in his office.”_

"Be right there."

John smiled, "Sorry Ronon, rain check on the good doc. Woolsey wants us in his office."

Ronon sighed and shrugged, following John towards the gate room.

oooooo

Rodney and Teyla were already seated by the time John and Ronon arrived; Rodney's irate voice echoing beyond Woolsey's office.

"How long is this going to take? I need to get back to my lab. I can't leave those pre-school scientists on their own for even a minute, they may blow something up!"

"I'm sure Dr. Zelenka can handle things for a little while Dr. McKay" sighed Woolsey. He lifted his eyeglasses up and squeezed the bridge of his nose with his fingers. "Ah, Col. Sheppard, Ronon, good you're all here."

"What's this about, Woolsey?" John asked, gingerly taking a seat.

"John, are you not well?" Teyla noticed the bruise on his forehead. "What has happened?"

Ronon smirked, "He ducked when he should have swerved."

Teyla looked at him confused.

"I'm fine, I'm fine!" John scowled at Ronon then turned to Woolsey and nodded.

Woolsey stared at him for a moment then nodded and continued.

"Teyla has been updating me on some of the planets the Athosians have visited over the years."

Teyla smiled continuing, "And I have heard through Halling that one of these planets have acquired something new that may be of great importance to your people. On the planet Kalthos, there is a city named Castima. They do not have technology such as Atlantis, but they are a quiet friendly people and it has been heard that they have acquired a miraculous medicine."

Rodney snorted rolling his eyes. "Voodoo nonsense."

"No Rodney," smiled Teyla. "From what Halling has heard, this medicine has been used by their healers to cure a handful of their people from a disease quite like the one on your planet. I believe you call it, Cancer?"

"What?! Oh please I…"

"Quiet Rodney!" John ordered. A cure for cancer?! It may be a fool’s run, but they had to go to find out for sure one way or another.

John turned to Woolsey "We can be ready in an hour."

Woolsey nodded his permission, reminding himself to order Col. Sheppard to the infirmary upon their return. He shuddered trying to imagine what it felt like to be hit by Ronon.

Rodney snorted again but rose with the rest of his team and they went to gear up.

ooooo

John felt the drop in temperature as soon as they stepped through the gate and shivered. The gate was in a clearing on a large hill surrounded by trees overlooking the city.

The wind was raging.

"Oh, I'm _so_ going to catch a cold!" groaned Rodney.

Ronon grunted scanning the surrounding area as he spoke. "It's not that bad, McKay."

"Whatever Sasquatch, I have a delicate system that needs balance…"

John rolled his eyes "McKay…life signs?"

"Huh, oh yes." Rodney pulled out the LSD. "No life signs nearby. The walls of the city must be made of some type of alloy blocking any life signs detection.

"Okay, let's get going then."

They headed towards the trees as John squinted up at the darkened sky. It looked like a major storm was coming and they needed to hurry to find cover in the city. He winced as a sudden jarring pain ripped through his head and vowed silently to practice Bantos rods with Teyla for a whole month before he dueled with Ronon again.

Behind him, Rodney sighed heavily looking up at the sky. "Great, just great." He pulled his jacket tightly together across his chest.

Teyla patted him on the arm then walked ahead.

ooooo

Just as they were about to enter the tree line John suddenly stopped and held his fist up, his team automatically crouching behind him. His spidey sense had started tingling.

"What? What is it?" yelled Rodney.

Ronon glared at him to stop yelling. "Sheppard?" hissed the Satedan.

"I'm not sure, something's off."

"There's...there's nothing. No life signs nearby, just us." said Rodney examining the LSD.

Over the sound of the wind came a sudden droning noise. At first faint then much louder. John squinted, peering into the trees, something was in there; something really bright and _really_ large and it was heading straight for them.

John subconsciously took a step back.

"BACK! Back to the gate!" he yelled.

As one they turned and ran back to the gate, Teyla and Rodney in front, John and Ronon behind, running backwards while firing at the encroaching light.

They were a few steps from the DHD when the light exploded from within the trees and slammed into them, disappearing in a flash a moment later.

The wind continued to howl in fury but the team didn't hear it.

They had vanished.

**TBC**


	2. Chapter 2

John woke up drowning.

Struggling to find some air he found he couldn't move, something was holding his face down in water.

_What happened? Did he crash the jumper in the ocean? Why was he in the water? What the hell was going on?_

A moment later he started to inhale, fighting for breath and losing it as a result. He felt his body start to slow as a tired heaviness crept over him.

_Is this it? Is this how I go out?_

Suddenly he was yanked backwards out of the water and onto hard ground.

John tried to see what was going on, but he couldn't get his eyes to focus, everything was one big blur.

"Ugghh!" He curled onto his side violently retching up water and what felt like his lungs, heart and all the other organs in his seizing body.

Then he was being dragged off the ground onto a heavy wooden chair where multiple hands started wrapping chains around his wrists, ankles, chest and neck.

John struggled to move but choked on the chain around his neck. Retching some more, he soaked the front of his chest and lap.

He leaned his head back against the chair spitting, trying to clear the bitterness from his mouth.

"Ah, the great John Shep Ard has awoken!"

_This can't be good._

John slowly opened one eye at the butchering of his name and peered in the direction the voice came from, his blurry vision slowly clearing. A stocky man in a dark woolen tunic stood in front of him

John opened his other eye and stared at the man without saying anything.

"What? No trembling, no begging?" asked the man grandiosely.

"No." John rasped, forcing a smirk that belied the concern he was feeling.

"The water was very refreshing. Thanks!"

The man laughed deeply and John winced. His head was pounding and he seriously began to wonder just how hard Ronon had really hit him.

"Ah…excellent. I love a challenge!" clapped his captor.

John slowly looked around. The room he was in was dimly lit except for a bright lamp blazing down over him.

His captor sat down in a chair across from him. Two other men stood guard in a corner of the room. Across from them John could make out a large basin of water.

_Ah yes, my alarm clock,_ he thought, shuddering inwardly. John turned back to his captor.

"Where's the rest of my team?"

His captor just smiled.

"Just tell me what you want!" John yelled.

"I want you, John Shep Ard. And I always get what I want."

"Well goodie for you, but I don't swing that way."

The man sneered and grasped John by the chin forcing him to look him in the eye.

"We shall see."

ooooo

Woolsey stood looking down at the gate room.

"Nothing yet, Chuck?"

"Sorry sir, no. Col. Sheppard's team has not checked in yet."

"They're three hours overdue." Woolsey sighed heavily.

_This did not bode well._

He tapped his comm. "Major Lorne?"

_“Yes sir?”_

"Please prepare your team."

_“Nothing from Col. Sheppard's team yet, sir?”_

"No."

_“We'll be ready in 15 minutes, Lorne out.”_

ooooo

"Rodney? Please…Rodney!"

He felt someone shaking him. Coming to his senses, Rodney slowly opened his eyes to see Teyla leaning over him.

He was lying on the ground near a Stargate, but not the one they came through to Castima. They were in the middle of a desert, the sun blazing high in the sky.

"Wha?"

Ronon appeared over him, a dark shadow blotting out the sun, his arm outstretched helping him to his feet.

"We need to get back to Atlantis now!” Ronon said.

"But…what's going...? Where are we?" Then it suddenly came back to Rodney. The terror he felt at John's yelled order to run for the gate. There was something else…the light. It sounded like a freight train! And...

_John_

_Where's John?_

"Colonel?" Rodney got to his feet "Sheppard!"

"He is not here Rodney."

"They took him!" Ronon growled. " _And_ our weapons and supplies!"

"This is not the gate on Kalthos, we must have been brought here while unconscious." Teyla stated. "Please Rodney, we must get back to Atlantis, come!"

_Would Sheppard ever catch a break?_ Rodney thought. They ran to the DHD and started to dial.

ooooo

Lorne's team was geared up heading toward the jumper bay when they heard the Stargate start up.

"Incoming IDC!" shouted Chuck. "It's Dr. McKay's!"

Woolsey strode from his office. "Dr. McKay, this is Woolsey."

"Lower the shield!" shouted Rodney. "We're coming in!"

Woolsey nodded at Chuck who lowered the shield as Lorne's team surrounded the gate, weapons raised.

Seconds later Rodney, Ronon and Teyla came rushing through.

Woolsey smiled and then frowned. _Where was Sheppard?_

He made his way down to the gate. "What's happened? Where's Col. Sheppard?"

Teyla stepped forward, "Sir, we need to mount a rescue mission right now. Col. Sheppard has been taken."

"By whom?" Woolsey was shocked.

"That's what I'm going to find out!" Ronon snarled.

"Are you all okay? You should be checked out first."

"There's no time!" yelled Rodney. "There was this light, like a train in the wind!"

Woolsey looked at him in confusion, Rodney waving his look away.

"We HAVE to go back NOW!"

Woolsey nodded towards Lorne and he and his team raced for the jumper bay followed closely by Sheppard’s team, less one member.

ooooo

John groaned trying to stretch his strained muscles while trying to ignore the sharp throbbing in his shoulder where his subcutaneous transmitter had been dug out and crushed in front of him. He had been stripped of his clothes and chained nude face up on a large wooden table.

Was that minutes ago? Hours? Days? There were no windows in the room and John was finding it harder and harder to keep track of the time. How was his team going to find him?

And why couldn't they have at least kept his boxers on?

_Damn he was cold._

Hearing the door open, John lifted his head slightly and watched as his captor came into the room followed by two other men; his guards from before, both also stocky and wearing dark tunics.

John lay his head back on the table and smirked at the ceiling.

_Frick and Frack._

"So any chance you plan on telling me what's going on?" John said with a sigh.

One of the guards walked towards him placing a large box near the table he was on. Then he proceeded to pull wires from the box and attached them to John's body.

Fear washed through John.

"Ah come on, can't we just talk about this?" squirming he stared at his captor. "Just tell me what you want. My people have a lot to offer you!"

"No, YOU have a lot to offer me!" hissed the man. He turned to the guard who had attached the electrodes to John and nodded.

Nodding back, the man turned a dial on the box and John's body arched off the table, his chains the only thing keeping him from flying off it.

The pain stole his breath away, his jaw clenching shut.

The guard lowered the dial.

"What is your name?" asked his captor.

"Puff the Magic Dragon." John rasped, eyes wide, breathing heavily.

His captor nodded and another surge of electricity raced through John who couldn't help but cry out.

"What is your name?"

"Luke Skywalker! My father's name is Darth!"

Another nod, another horrifying agony.

"What is your…”

"Lt. Col John Sheppard…S-Stop!" John couldn't understand. His captor already knew who he was, why was he asking for his name?

"No, it's not." smiled his captor. "You have no name."

"What?" John's vision greyed as another surge spread through his body.

"You _have_ no name." smiled his captor. And when the next surge of electricity ran through his body, John followed it into darkness.

**TBC**


	3. Chapter 3

The Atlantis search party held a meeting with the senate from Castima in the meeting hall of their city. The Castiman leader, Raylan Emitan was shaking his head gravely.

"I am truly sorry, but we have no knowledge of the whereabouts of your man. Though, we will of course help you in any way we can to find him. This bright light you spoke of, do you know its origin?"

"No," said Teyla. "We were enveloped by it a few minutes after we came through the Ancestral ring.

Raylan nodded. “We do have many travellers to our land that may have the capability of using such technology. We have heard stories about travellers visiting other planets, their only purpose to abduct the poor citizens for their own nefarious needs. Maybe the light you speak of is one of the ways they accomplish this."

"So, why didn't they take all of us?" asked Rodney haughtily.

"I am sorry, I do not know. We can however provide you with the names of several planets where we have heard that these criminals have frequented."

"That would be helpful." said Lorne. "You do understand we will need to search your city before we go?"

Raylan nodded, "We have nothing to hide and do not wish to make enemies of Atlantis. Our city is your city."

Lorne radioed in and a few moments later two jumpers flew from the gate spreading out and started scanning the city and planet for John; eyeing their scanners for any sign of his subcutaneous transmitter.

ooooo

_6 days later._

After his second escape attempt, John had been thrown into a tub of freezing water and held down until he was sure that he was going to shatter and die, then gasping he was pulled from the water and slammed up against a wall.

They had fed him only twice since his capture; a measly meal of some type of porridge and stale water. So he had no energy left but to struggle weakly in vain as he was held with ease against the wall by one of the guards.

The concussion John finally recognized he had, had made any clear thought an almost distant memory.

He was aware long enough to notice the other guard pulling on gloves that glinted of metal in the low light. The guard smiled at him viciously then started the assault. To John every blow, every punch felt like his organs were being crushed.

_What the hell were they doing to him!?_

A fist to the head threw him into oblivion.

ooooo

John's eyes fluttered open. He lay curled in a fetal position in complete darkness, the cold ground beneath him, his nude body cramping from the cold hardness subjected to it. John lay staring into the darkness for a while swallowing repeatedly trying to keep the nausea that bombarded him from spewing forth. Suddenly, he came to himself the horror of a thought finding its mark.

_Did they blind him?!_

He touched his eyes waving his hand in front of his face.

Nothing.

John started panicking his hand inching forward in the darkness.

"Hey!" he coughed. His throat felt like sandpaper.

"HEY!" His hand inched across cold bricks then touched rough wood.

A door.

After a few minutes he realized that they had him in some type of closet. Feeling for the door knob he yanked.

Nothing. He was locked in.

"Hey!" John pounded weakly on the door; a very small hole in the wood easing his mind somewhat. There was a faint light coming from the other side. He wasn't blind after all. He slid down the door, a sob escaping from him. How long had he been here? Where was his team? Were they looking for him? Were they dead?

John closed his eyes and silently wept.

_Come on guys…please find me._

ooooo

Radek watched Rodney over the top of his computer. It had been four weeks since Col. Sheppard's disappearance and he was beginning to worry about his friend. He flinched at the sound of Rodney's coffee mug being thrown against the wall.

"Dammit!" Rodney pulled his hand through his dishevelled hair staring at his computer screen. "I don't...I don't know…"

Radek sighed and walked over to his friend. "Rodney, you need to take a break. Go get something to eat. I will continue with this." He gestured at the screen.

"Go away Zelenka, I'm fine!"

"No you’re not, Rodney."

Rodney spun around in his chair and faced him.

"We've searched EVERYWHERE for him. He's not on Castima, we couldn't find any trace of him on any of the planets the Castiman leader told us about! We've checked all fifty planets that were last dialed by the DHD…and NOTHING! It's up to ME to find him, don't you understand? I can do it! I'm smart enough, I can figure this out!"

Radek's fears must have shown in his eyes, because Rodney shot up from his chair.

"NO! He's not dead! He's not! So just leave…leave…" Rodney swayed.

"Rodney?" Radek grabbed him by the shoulders. "Rodney!"

Rodney's eyes rolled in his head and he slipped to the floor soundlessly.

Radek tapped his comm. "Dr. Beckett!"

_“Beckett, here.”_

"It's Zelenka, please come to the lab. It's Rodney."

_“Aye, I'll be right there.”_

ooooo

He didn't know what anything was anymore. Up, down, life, death.

Nothing except darkness.

And pain.

His captor looked up from the console at his newest acquisition. The powerful gene carrier would make his city triumphant in becoming the majestic city they were meant to be. The few ancient weapons still working from the last, now dead gene carrier helped bring this one here. However, the more powerful ancient weapons lying dead in their city's bunkers would come to life under this man's power. Then nothing would get in their way. One day they would rule the galaxy.

His acquisition floated in front of him in a large tank of water, nude, electrodes all over his body; a breathing apparatus in his mouth, a darkened visor covering his face.

"Let us begin."

A turned dial on the console and John's world exploded.

His captor watched as John jerked violently in the water. Then he spoke gently into a microphone linked to the visor John wore.

"Atlantis is your enemy. Our enemy. They have slaughtered our people. They killed your family, your friends, and your children. They tortured you..."

He pressed a button and John jerked again.

Lights strobed like daggers through John's eyes, then a flash of a large man attacking him, knocking him to the ground. The man loomed over him like a mountain, his hair long twisted dark strands. He knew this man…his name…what was his name? The man grinned feral like and stretched for him. John jerked back.

"They will use you against us if they have a chance. You are our protector. You protect the children, you are all we have. They will destroy us all if you allow it. You are our Soldier. You must protect us or the children will die."

_Flashes of children running through a desert laughing, men in uniforms running towards them then an explosion and screams of blood, small body parts lying everywhere…_

John gasped struggling in his floating prison; the flash of memory from his time in Afghanistan invading his mind.

_Oh God, No!_

Five hours later when John was pulled from the tank his eyes were glazed over, the spark gone.

ooooo

The infirmary waiting room felt cold and barren. Teyla sighed as she sat staring at the floor.

First John, now Rodney. Their team was truly being tested. Ronon leaned against the wall twirling his blaster in his hand a heavy frown on his face.

Carson walked in and sat down next to Teyla.

"Dr. Beckett, how is Rodney?" she whispered.

Carson sighed heavily. "He's suffering from malnutrition, and he's dehydrated. I have him on fluids."

"Can we see him?"

"Uh, yes love. Though we had to sedate him and…" Carson lowered his eyes. "And restrain him."

Ronon put his weapon back in the holster and scowled. "Restrain him, why?"

"He was struggling to leave; he said he had to get back to his lab to continue his search for Col. Sheppard."

Ronon growled then turned and stormed off.

"Ronon!" shouted Teyla, but he ignored her. Teyla turned back to Carson nodding slightly. "Please, take me to Rodney."

ooooo

Rodney's face was turned to the wall as Teyla walked up to his bedside.

"Hello Rodney, how are you feeling?" Teyla smiled grasping his hand.

Rodney turned to her, his blue eyes dull and glazed. He pulled weakly at the restraints. "Teyla, let me go. I have to find John."

Teyla smiled sadly. "We have not given up on him Rodney, we will find him."

"Not without my help. You need me."

"Yes, we do. But we need you well. Please rest, let Dr. Beckett help you."

Rodney yanked his hand back and turned away from her. "Just go away."

"Rodney."

"If you're not going to help me, go away!"

Teyla sighed sadly then pulled up a chair.

ooooo

Woolsey was talking to two gate technicians when Ronon stormed into his office. All three men took a step back. Ronon was like a wild man.

"Woolsey!"

"Thank you gentlemen that will be all." The technicians scurried out giving the Satedan a wide berth.

Woolsey took a deep breath. "What can I do for you Ronon?" he returned to his desk straightening his uniform as he did.

"Let me through the gate, I'm going to find Sheppard."

"It's been four weeks. We've searched all fifty planets. We don't know where he was taken Ronon, he could be anywhere. He could be…"

"He's not dead! I would know it. Let me go back out there and look. I’ll bring him back."

Woolsey stared at him. If anyone could find the Colonel, Ronon could. "Lorne's team goes with you."

"No, I can go faster on my own."

Another beat. "Go bring our man home."

Ronon flew from the room to prepare.

ooooo

Teyla tried to find a comfortable position in the hard infirmary chair. She glanced at Rodney who was sleeping fitfully finally giving into the sedative. Her comm rang…

"Teyla."

Ronon stood in front of the gate. _"I'm going to find him, Teyla."_

"Ronon...?" She wanted to help him, go with him.

But she couldn't. She needed to stay with Rodney.

"Bring him back Ronon."

_"I will. See you soon."_

"May the Ancestors be with you."

Ronon turned his comm off and strode through the gate.

**TBC**


	4. Chapter 4

John was swallowed in utter and complete loneliness.

He had been left alone for so long that he had begun to long for the sound of his captor's voice. A bark of laughter at that thought echoed from his raw throat and bounced off his prison walls. He felt something was slipping away from him, but he couldn't grasp what it was. When his captor had finally come bringing him some food, water and clothing to wear, he almost hugged the man in tearful gratitude.

Finally clothed and somewhat satiated; John lay humming on his small cot, painfully aware of the voice coming through the vent to his room.

He was trying to drown the sound out with his humming, but to no avail. It had been saying the same words over and over for every second of every indeterminate moment; John felt the words skitter across his skin into his mind, into every ounce of his being. He tried to ignore it, but the words soon formed his existence...

_I am no one, I am Soldier, I am no one, I am Soldier._

Soon he found himself whispering the same words, again and again. Like a frightful mantra. He couldn't stop himself.

Then suddenly, he had company. The guards came carrying a syringe. John's heart dropped as he tried to scurry into a corner of the room.

"Please, no." he whispered. But there was no strength in it. He was alone. He was…his name was...was…

He sighed heavily as a guard held his arm out as the other injected him.

John grabbed one of the guard's arms as they stood.

'Wha-what am…who am I?"

The guard grinned at him.

"You are Soldier."

Then they turned and left and John lay curled in a corner of the room screaming as the serum flowed through him like a hungry beast.

ooooo

Two days later, the captor stood outside the locked door smiling. The screams coming from the other side of the door had been gaining momentum, telling him the serum was working its magic. He opened up the view hole in the door. His soldier was writhing on the floor grabbing his head and banging it on the ground.

"No! No! Stop!" John screamed.

He dragged himself to his feet and started pointing and screaming at the air. "Stop! STOP! I'll kill you…I'll kill you all!"

John threw himself against the wall and started battering it with his fists. "I'll kill you all!"

The captor closed the view hole. The injections were working.

His people had come across this miracle drug on their travels. They thought it was a cure for the disease that was killing many of their own, but they were wrong. Their sick died of their disease, but not before a very interesting side effect was noticed. The drug's side effect? It made the patient both compliant and violent all at the same time.

Raylan Emitan smiled.

It was time for his Soldier to get to work.

ooooo

_Four months later_

Ronon had returned to Atlantis empty-handed. It was like Sheppard had vanished from existence; all leads to his friend proving false. From planet to planet, from connection to connection, from back alleys to darkened pubs, from threat of Ronon's rage, no one had seen the Colonel. Ronon would have kept looking forever but had returned begrudgingly at Teyla's request. Some new information had come to light.

ooooo

Teyla, Rodney and Ronon sat in Woolsey's office.

"I believe we should check this out, sir." Teyla stated.

They were discussing the recent success of attacks that the city of Castima had on other planets. They had gone to M59-PX0 to the city of Lema, after hearing it was one of the cities that Castima had attacked. It had been a quaint city that the Athosians had traded with on a few occasions.

Now a quarter of the city lay in ruins. The Castimans had laid ruin to the guard barracks and homes of the leaders; more than one hundred dead. Blood had poured in the streets leaving the city leaderless and defenseless; ripe for any warring faction to come in and take over.

"As long as I have known them, the Castimans have not been a violent people. It is strange that they would go on the attack with no provocation. It is surprising with their lack of technology to have succeeded in so many victories."

"Well, what are we waiting for?" asked Rodney incredulously. "This can't be a coincidence. Castima was where we lost Sheppard. We have to go back!"

Woolsey held his hand up to quiet Rodney. "I agree Dr. McKay. This needs to be checked into."

Ronon was already up and out the door before he could finish his sentence, Rodney and Teyla following quickly behind.

Woolsey rubbed his brow trying to keep his hopes at bay that this was a sign that would point them to the whereabouts of Col Sheppard. He didn't know if he could stand the disappointment if they came back empty handed once again.

ooooo

Soldier had no need for locked doors anymore. Free to walk around the city, Raylan walked with him regaling him of the beauties of Castima.

He stood out with his raven black hair against the pale orange hair of the citizens; his tall lithe muscular frame different from their shorter wider frames. He was different, he was special. He was Soldier. That was who he was and what he was. His reason to exist was to save his city and his people. And to Raylan's satisfaction and amazement he had already proved his worth.

After showing Soldier the underground storage bunker, many of the dead ancient weapons stored there over many generations of secret trading and theft had been brought to life under his hands and Castima was feared once again. They would no longer be the city that people didn't think twice about. If Raylan had anything to do with it, Castima would go down in the history books as the most powerful city in the Pegasus Galaxy. Their reputation was growing mile by mile, death by death. Raging against city after city they had come out victorious every time.

Soldier was well revered. Every few days he was given the serum, his "medicine" to keep him in line and it was working amazingly well. The pain of the first few injections was now a thing of the past as his body had gotten used to the drug and now welcomed it.

Sitting down for their evening meal, Raylan smiled as he watched him eat.

Soldier smiled back at him, "What is it?" he asked.

"You have helped your people achieve victory time and time again, Soldier. As we speak, some of our guards are taking over the latest of our conquered cities in the name of Castima. However, we have another city to triumph over.

His Soldier waited expectantly.

"Atlantis" Raylan silently held a breath staring into the gene carrier's eyes. This was the ultimate test.

"Atlantis?" A sudden fury burned in Soldier's eyes. Flashes of dead children and the corpses of a family that he could not remember but would avenge flew through his mind.

"The very one. The Lanteans have heard of our triumphs and are getting ready to strike against us. We must strike first."

Soldier pushed his plate away his eyes grim and deadly.

"So, what are we waiting for?" He nodded at Raylan and headed off towards the bunkers and the ancient weapons storage.

Raylan leaned back in his seat and smiled.

ooooo

The next day found Raylan Emitan pacing the meeting hall angrily. The Lantean people had returned, they were going to ruin everything!

He was told more of their space crafts were scanning the city. The weapons bunker was well hidden. He didn't expect them to find it; but was grateful that Soldier had gone off world with some of his men to gather info on another city on their list that they had planned to attack. He had not "versed him" on the true power of Atlantis and had needed a few more days. But now _they,_ had to come.

"You are a peaceful people" smiled Teyla diplomatically. "We are just trying to understand why you have been attacking other worlds."

"And winning..." Lorne continued, patting his P-90.

"We are not as peaceful as you may have heard. We have an excellent military who have been training for many months to protect our kind from violent outsiders."

"That's great." said Lorne, "But you haven't been attacked, you've been doing the attacking."

Raylan could barely hold back his fury.

"You saw what an outsider did to your people when they came through the Ancestral ring. It could have happened to any of my people. What if it was our women and children who had come through the gate on the way home from trading? We will not be a victim in our own land! How dare you come here and question us! We have done nothing to deserve your mistrust! You must leave, now!" He nodded at his guards and they raised their guns and aimed.

Ronon growled, pulling his blaster out.

Lorne and his team aimed back with precision, but they were far outnumbered.

Raylan smiled at them, his eyes deadly.

The guards took a step forward.

After a moment, Lorne grimaced and said, "Stand down!" He lowered his weapon his team following suit. "Ronon, stand down! That's an order!”

"Where's Sheppard! What have you done with him!?" Ronon shouted, his blaster still raised.

Raylan looked at them blankly. "Shep Ard your leader? I have no idea where he would be"

"Ronon." warned Lorne. Ronon lowered his weapon and turned to Lorne. "He's lying!"

"We're leaving, now!" said Lorne. The Lanteans slowly backed out of the hall and headed for the gate.

"Ronon is right." said Teyla. "He is lying."

"Yeah, I know." said Lorne "We're not giving up on the Colonel. Not this time." He tapped his comm. "Jumper one, jumper two. Stealth mode. We're heading back through the gate. Keep scanning."

" _Copy that, sir."_

" _Copy."_

The team had just come through the woods to the clearing where the gate stood when it activated.

"Incoming." Lorne yelled. "Scatter!"

The Lanteans made for the edge of the woods using the trees as cover. A few moments later a small group of armed men came through the gate laughing and patting each other on the backs."

"Some more Castiman guards." Lorne whispered.

Rodney peered around the cover of the tree he was standing behind. His hand grasping his weapon so tight his knuckles were white. One of the guards looked different than the others. He was taller, slimmer and his hair…it was…it was…

_No it couldn't be!_

He pulled out his binoculars and felt his heart stop beating.

_It was Sheppard._

Rodney stepped out into the open.

"Sheppard!"

The group of men stopped. as one their guns raised. Rodney took a step back. "John?" he gulped.

"Lanteans!" one of the guards shouted.

John took a step forward and opened fire.

ooooo

Lorne's team, Ronon and Teyla emerged from the forest and returned fire, the guards and John scattering to take cover. Rodney had dropped, belly to the ground covering his head with his hands.

"Don't shoot him!" he yelled. "It's the Colonel! It's Sheppard!"

Teyla glanced up from where she had taken cover in time to see John duck behind a nearby large rock.

"Rodney is correct!" she yelled out to the team.

"John, it is Teyla! Stop shooting!"

Lorne's team had taken out the other guards. Teyla had pulled Rodney to cover and had turned to see Ronon running towards the edge of the trees. She nodded to herself. He was going to try and go around and come up behind the Colonel.

This was not supposed to be happening! Lorne thought. What was Sheppard up to?

"Colonel!" He shouted, "It's Major Lorne, sir. Stop shooting!"

John's voice echoed back from across the clearing.

"You're earlier than expected! Throw down your weapons and tell your men to come out with their hands raised. You made a big mistake coming here!"

John leaned against the large rock he was using for cover and smiled as he pulled a dark metallic strap from his pocket and wrapped it around his palm. A small glowing red orb appeared and hovered in his palm. If it was good enough to take out the Lemans it would be more than sufficient for this small attack team.

He stood from his hiding place and opened fire on the team as they scurried to hide, he crouched and ran to the trees at one end of the clearing and started to make his way closer to the invaders. A minute later, he could just make out one of them.

Smiling, he raised his hand. The orb grew into a large crackling ball of light and he was just about to launch it at them when he felt a surge of electricity shoot through the shoulder of his gun arm. The gun flew from his grasp into the brush. His legs gave out from him and he collapsed to the ground. John slowly turned over to see a wild man pointing a weapon at him. The man looked familiar, he… John had a flash of the wild man attacking him then leaning over him with a feral grin.

"Sheppard, it's me!"

John growled and started to raise his weaponized hand toward the man when the man shot him again and the world fell away.

ooooo

The activation of the gate drew Woolsey from his office.

"Incoming IDC, sir."

Woolsey looked at Chuck expectantly.

"It's Major Lorne!" smiled Chuck.

Woolsey turned toward the gate. "Major, what's your status?"

"We're coming in sir, have the medical team ready."

"Of course."

Woolsey turned to Chuck who lowered the shield, then he tapped his comm. "Dr. Beckett, to the gate room with a medical team, stat."

_“Aye, on our way.”_

Moments later Lorne and his team came through the gate followed by Teyla and Rodney.

"What happened?" asked Woolsey. They all _seemed_ okay.

"Is anyone hurt?"

Rodney and Teyla turned back to the gate just as Ronon came through carrying a uniformed man across his shoulder. "What's happened, who is that?"

Teyla smiled at him but with worry filled eyes. "It is Col. Sheppard. We have found him."

Woolsey turned to the unconscious man. It was indeed the Colonel.

The medical team arrived at that moment, Carson gasping when he saw who the patient was.

"Ah, son…" he patted John's shoulder.

"What happened?" he asked the away team as his orderlies put John on a gurney and whisked him away.

"I shot him." muttered Ronon gazing down.

Both Woolsey and Carson turned to him.

"You what?" they said in unison.

Lorne sighed. "Col Sheppard came through the gate with some Castiman guards, then opened fire on us."

Ronon pulled a metallic strap out of his bag. "He was going to use this on us. It's Ancient".

Carson shook his head in disbelief then ran after the departing gurney.

Rodney held his hand out to Ronon, "Give it to me, I'll examine it in the lab." But Woolsey took it from Ronon instead.

"No, Dr. McKay. I'll let Dr. Zelenka look into this." He looked the away team over. "All of you get yourself checked out in the infirmary."

Rodney, Teyla and Ronon didn't need to be told twice. The infirmary was where Sheppard was. Lorne and his team followed behind; worried, but with smiles on their faces.

They had their leader back.

**TBC**


	5. Chapter 5

_**Atlantis smiled, the gene carrier had returned. She had missed his presence. But something was wrong with him! Atlantis flickered, then powered up again. She would be ready when he needed her.** _

The infirmary lights flickered overhead, unnoticed by Rodney who sat quietly, his eyes never leaving the body of his best friend and leader. He was waiting for John to move, twitch, sneeze, ANYTHING, but he just lay there like he was dead.

"Come on John." he whispered

The privacy curtains behind him pulled back and he heard a heavy sigh.

"Aye Rodney, come on lad you need to get some rest."

"I'm not going anywhere Carson."

"You've been sitting there for two days straight! I'll let ye know when he wakes up, believe me."

"No." he swiped quickly at the hovering tears that threatened to come.

"Fix him Carson, please…just fix him."

"Aye lad, we're doing our best."

The blood tests had come back the day before. A foreign substance was found in the Colonel`s blood which they were still running tests on. They could not figure out yet why he had not regained consciousness.

"Where is Teyla and Ronon?"

"They went to get something to eat." Rodney whispered. "Said they'd be back shortly."

Carson pulled up a chair and sat next to him, placing his hand on Rodney's shoulder as they both watched John's chest slowly rising up and down.

It was almost hypnotic; nothing existed except this subtle sign that their friend was still alive.

ooooo

Another day passed. The infirmary was quiet when John crawled heavily from the darkness that held him. He felt the pain rippling through his body before he tried to open his eyes and groaned softly.

His team who had set up camp around his bed speaking quietly to themselves, got to their feet.

Teyla, nearest to the top of the bed caressed John's forehead.

"Col. Sheppard, can you hear me? Please open your eyes."

John's eyelids fluttered and he groaned again.

"Please John, we are all here for you, we need you to wake up now."

Then slowly for the first time in months, his team saw the mossy green of his eyes as he strained to open them.

"That is good John!" Teyla continued.

Rodney couldn't help but laugh out loud. His friend was back. He turned to move the privacy curtain aside. "Carson!"

Ronon standing near the foot of the bed was grinning from ear to ear. He grasped one of John's legs and gave it a slight nudge.

"I knew you were lazy Buddy, but even this was pushing it!"

At Ronon's touch, John's eyes flew open all the way and with a guttural yell he sat up in bed.

Teyla reached for his shoulders to steady him and he pushed her arms away, scrambling back in the bed until his back was against the walls, the i.v. poles and wires straining to match the distance.

Ronon's smile slowly faded. "Sheppard?"

John stared at them, his face blank, his eyes dark with confusion and an almost madness.

Rodney stepped towards the bed one hand held up, "John, it’s okay! It's us! Relax you're safe back on Atlantis!"

His words disappeared from mind as at that split second John dove off the bed right at Teyla. Wires were yanked from his body but he showed no sign he felt it. Grabbing Teyla in front of him he held her in a choke hold, his arm tightly across her neck and started to shuffle backwards away from the rest of his astonished team.

Rodney was suddenly scared. When John looked at him _through him_ he realized there was no recognition in his eyes. Only fear. And John Sheppard did _not_ do fear.

"Sheppard, it’s us." he whispered and took a step towards his friend.

John took a step back tightening the hold on Teyla's neck.

"John!" Teyla choked, struggling to break his grip.

His eyes flicked everywhere in confusion.

_Where was he? This wasn't Castima!_

Then he remembered what the man had said.

_On Atlantis…He was on Atlantis!_

With his free hand he went for his gun, finding nothing he glanced down; they had taken his weapons and his uniform and put him in some flimsy clothing. He couldn't face them like this, unarmed and unsteady.

At that moment Carson came out of his office.

"No need to yell Rodney, what's all the ruckus..?" He froze as he saw what was happening then glanced at Ronon as he saw the tall warrior slowly reach for the blaster on his hip.

He quickly shook his head. He didn't know what a blaster would do to John's recuperation. It may have been the reason along with the foreign substance in the Colonel's system that kept him unconscious for so long. Ronon grimaced but removed his hand from the weapon.

"John, lad why don't you just…"

John didn't even hear him, all he saw and understood was that he was slowly being surrounded and he had to get out of there. He let go of Teyla and violently shoved her towards Carson, they both sprawled to the ground as John turned and ran for the infirmary doors.

Ronon's legs were longer though and in two steps he reached John and grabbed him by the shoulder spinning him around only to receive an elbow to the face as John retaliated. Shaking it off quickly, he grabbed John around the waist pinning his arms and lifting him off the ground.

"Sheppard, calm down! I don't want to hurt you!"

John growled and head-butt Ronon who let him go as he reeled backwards crashing into a glass cabinet, blood gushing from his nose. John glared at him in satisfaction. Glancing down he spied a scalpel that had been thrown from the cabinet. He smiled grabbing it, then spun towards the door only to find someone else standing in his way.

Rodney swallowed heavily as he faced John. "Come on Sheppard, you know I'm not good at this stuff! Just-just lay down, we're not trying to hurt you! Go lay back down!”

John snarled and lunged at him scalpel held high, but was tackled to the ground by two large orderlies who had heard the noise of Ronon crashing into the cabinet and had rushed in.

It took both orderlies and Ronon to drag John kicking and screaming obscenities off the floor and back onto the bed and Carson now back on his feet rushed to attach restraints. Teyla and Rodney looking on in shock.

Seconds later they all took a step back from the bed, leaving a very angry red-faced Colonel twisting and raging, convulsing his body trying to break away the bonds that held him in place.

Carson stepped back to the bed, he couldn't stand seeing his friend like this. He touched John's arm. “Please lad, we're tryin' to help ye. Please…"

John suddenly stopped moving, looked Carson in the eye and whispered something.

"What lad?" Carson moved closer, his face inches away from John's.

John spit in his face. "Murderer!"

He started struggling again as Carson stepped back eyes wide hand to his face, then turned and strode to his office slamming the door behind him.

All the others could do was stand by and watch their leader struggle, hoping against hope that he would eventually pass out from exhaustion.

It took hours.

ooooo

"Dr. Zelenka, please explain to the others what you told me." Woolsey nodded at Radek who sighed pushing his glasses up on his nose. He looked around Woolsey's office. Col Sheppard's team, Major Lorne and Dr. Beckett stared back at him. They looked drained with worry.

Radek placed the metallic band that John had worn on Woolsey's desk.

"You have found out what it does?" asked Teyla

Radek nodded sadly. It has an electrical charge that builds up in it, but one that we have not seen before. From what we could gather, when the charge hits someone, it..."

"It what?" asked Rodney.

"It doesn't just electrocute the person, it tears them to shreds. A most awful and bloody way to die."

There was a moment of silence as they all took in the information and what could have been if Ronon hadn't fired on Sheppard first.

Woolsey broke the silence turning to Carson. "Has Col. Sheppard said anything yet?"

"I'm afraid not. It's been days and he just lays there staring at anyone who comes near him. I have never seen such hate in someone's eyes."

"He has allowed me to feed him." smiled Teyla. "That is a good sign is it not?"

"Yeah, but only because Carson threatened to tube feed him." said Rodney. "Sheppard may not be Sheppard right now, but he still wouldn't allow that to happen to him."

Woolsey gently pushed the metal strap to the far corner of his desk. "This can't go on." He turned to Lorne. "Is there any news about Raylan Emitan?"

Once John had been found and returned to Atlantis, a military team had returned to Castima arresting the military leader and the senate under Raylan's command. Raylan was nowhere to be found.

"That man is responsible for what happened to the Colonel. I don't need to tell you how urgent it is that we find him."

Lorne stared at Woolsey eyes sparking with anger over what had been done to John.

"No sir you don't. We _will_ find him. You can count on that."

Teyla stood. "If you excuse me, I am going to get the Colonel his lunch."

Dr. Beckett stood. "Aye love, I'll come with you."

The meeting over, they dispersed each of them eyeing the metal strap; the weapon of death their friend held with malice in his heart.

ooooo

_**Atlantis was confused. The gene carrier had not reached out to her since his return. He was in a weakened state. She would try to strengthen the link.** _

Soldier's patience was wearing thin.

Recently he could feel an underlying thrum racing back and force through his body; like he was constantly in some sort of static electricity field. He felt at odds like someone was talking to him but he couldn't quite hear what they were saying. He wondered if his captors were drugging him. It wouldn't work. He was Soldier and far stronger in mind and spirit then the murderous Lanteans. He had only allowed the woman to feed him because he needed his strength back to escape. She sat there smiling at him as she fed him another spoonful of a blue chewy concoction. His face soured at the texture.

"It is jello." the woman said. "You love it, especially this blue one. Do you remember, John?"

Soldier cocked his head, eyes narrowing. They kept calling him by another name. It was most likely to try and confuse him in his weakened state. But he was not as weak as they assumed. He'd play along until he could find a way to escape.

"I know you" he stated.

The woman froze, the spoon halfway to his mouth.

"Yes John, I am Teyla. We are good friends."

Soldier subtly looked around, they were alone in the room. "Of course, I remember. Teyla, why am I tied down? Please, let me go." he smiled and gave her his most innocent wide-eyed look.

"You remember me?"

"Of course!"

Teyla put the spoon down. "What is my child's name?"

Soldier hesitated. “Your child?"

"Yes."

He stared at her smiling, then lunged… his face morphing in utter rage.

“YOUR CHILD?! I AM SOLDIER! WHAT USE DO I HAVE FOR A MURDERER'S CHILD'S NAME? LET ME GO! OR I WILL END YOUR LIFE IN THE MOST HORRIBLE WAY I KNOW HOW!"

Teyla quickly pushed back in her chair moving away from the bed. John was restrained but he could still do damage to her if he tried.

"Murderer? Who have I murdered, John?"

Soldier glared at her gnashing his teeth, then suddenly collapsed back on the bed his face a mask that Teyla could not read. He turned his head and closed his eyes.

"John, tell me. Who have I murdered?

Teyla could just hear him whisper, "You killed the children. You killed my family. I will wash in your blood before this is over."

**TBC**

**Notes for the Chapter:**

> The story is at the halfway mark. I'll post the remaining five chapters in the next day or two after some editing. I'd love to know what you think so far!


	6. Chapter 6

“This is ridiculous.” huffed Rodney quietly. “We're treating him like he's a criminal!”

Rodney, Teyla and Ronon watched from a corner of the infirmary as John stood next to his bed surrounded by four guards, one of them handcuffing John's hands behind his back.

"I agree Rodney." whispered Teyla, "But we know what the Colonel is capable of. This is just to ensure his safety."

"This is a bad idea." stated Ronon.

Carson stood by his office door watching, then walked over to John's team.

"Keep an eye on him." He nodded towards John. "He's developed a slight fever since last night and his most recent blood test has shown that the substance in his blood stream has started to break down."

“This substance, is it to blame for Col Sheppard's unrest?" asked Teyla.

“Aye, I believe it is one of the reasons the Colonel is like he is. But he was gone for so long, we don't know what else was done to him."

"Should he not then remain in the infirmary, Carson?"

Carson sighed. “He needs to come back in a few hours so I can check on him, but for now he's doin' no good here. He needs to be out there in familiar surroundings. We've gotten nowhere trying to trigger his memory with him tied to a bed. This could help him."

"Or cause him to freak out again." muttered Ronon.

“Yeah.” whispered Rodney. "What'd he say, Teyla? That you killed the children and his family? What's that about?"

"Rodney not now, we will understand once John is able to talk about it." asserted Teyla.

"Yeah for now, we'll just have to deal with a violent sociopathic leader who hates us and wants to wash in our blood... goodie." muttered Rodney.

The guards stepped away from John surrounding him in a circular formation.

The lead guard turned to the group in the corner and nodded. They were ready to go.

They moved towards the door, John walking in the middle of them eyes straight ahead. His team followed behind them, hoping that once he saw his quarters that maybe something would click and "their" Sheppard would start to emerge.

ooooo

When the healer had told him about being moved out of the infirmary Soldier hid the darkness that was forming on his face and smiled at him thanking him.

The man had looked thoroughly confused over the thanks.

Now he was being marched down a hallway like a prisoner being led to execution. He didn't believe these people would kill him, not yet anyways. They had interrogated him about Raylan and wanted to know more about Castima. However, he had ignored their questions. He would not give up his friend and mentor to the Lanteans. He would die before he did that.

The guards that surrounded him seemed uncomfortable, like they preferred to be anywhere but guarding him at the moment. Soldier took note of that.

During his march, he noticed Lanteans standing off to the side of the hallways whispering to each other, watching him, pointing at him.

Soldier felt the rage boiling inside of him. He would not retaliate though.

Not yet…Not yet.

ooooo

Shortly they arrived at a doorway in a quiet corridor. Two guards stayed at the door as the other two entered into the room with Soldier followed by his "team".

The lights automatically came on in the room. Soldier did not notice the guards and the "team" giving each other knowing looks at that.

A guard uncuffed him then stepped back, hand tightening on the weapon he held against his chest. Soldier pretended not to notice.

He slowly walked around the room stretching as he did, touching an item here and there.

"So this is my new prison? My home in Castima is much cozier."

"Castima was where you were held. _This_ is your home." smiled Teyla.

Soldier looked at her with blank eyes and then he smiled and continued perusing the area.

"Why all of this?" he asked. "You weren't so kind to me the last time you held me prisoner. "

"We are your friends Colonel, we have never held you prisoner."

Soldier, his voice empty of emotion looked at her. "Yes you did. You kept me away from my people…you kept me away just long enough."

The way John spoke caused shivers to run down Teyla's spine. She glanced at Ronon and Rodney who looked like they felt the same way.

Teyla walked over to the Johnny Cash poster over the bed.

"Do you recall this man, Colonel? You call him the man in black."

Soldier chuckled. "Why do you call me Shepherd? I'm not a Shepherd. I am Soldier."

"You're John Sheppard. That's your name." growled Ronon from where he stood leaning against the wall by the door.

Soldier just blinked at the warrior then turned looking randomly through a book on the table.

“That's "War and Peace." said Rodney. “You've been trying to read it. Though it's taking you a ridiculous long time to actually fi…." Rodney caught himself. He was babbling, he knew it.

Soldier blinked again his eyes slightly unfocused as he looked around the room.

“Could be a little brighter in here."

The lights in the room automatically flared and grew brighter.

Soldier frowned, eyes narrowing, his mind racing trying to sort through what had just occurred.

Rodney coughed and stepped forward hoping to distract John from his obvious line of thinking.

He pointed at some dvds on the nightstand next to the bed.

“Uh, these are some of the movies you like to watch. We uh...we watch the movies together...all of us…in the movie room."

No response from John.

Rodney gestured, "The washroom is just around the corner. You've got beer in the fridge." He patted a bag in the corner of the room. "And your golf clubs are right here."

“Gulf clubs?"

"No Sheppard, golf…golf clubs. You love the game, told me you played it a lot back home when you had the chance."

"I've never played gulf." scowled Soldier. "I've been too busy protecting my people."

“Yes, yes, you've protected us all, but you do occasionally have some down time!"

“Protected you? Don't be ridiculous. Why would I want to protect you? I'm talking about my _own_ people."

"We are your people, Sheppard! Can't you get that through your thick head? What the hell did they do to you?" shouted Rodney.

Anger flared in Soldier's eyes and he took a step towards the insolent man. Rodney took two steps back and the two guards in the room stepped forward hands tightening on their guns.

Soldier smiled cunningly, his hands held in mock surrender.

"Relax, Rodney." He smiled and turned to the others. "Teyla, Ronon. Why don't we all just relax?"

His team stared at him at odds with their feelings. It felt good to hear him say their names, but John's eyes told another story, that he didn’t know them...or cared to know them.

Ronon held his blaster low in his hands. "We know you don't remember us, Sheppard."

Soldier held the back of a chair as he stared at the warrior. Smiling he tilted his head slightly and squinted his eyes.

“Sure is bright in here..."

Then he thought as hard as he could…

_Lights off!_

The lights in the room automatically clicked off leaving the room in complete darkness.

Ronon growled and raised his blaster aiming it where John had stood, and just as he was about to fire he got a chair to the face for his troubles.

Chaos ensued.

Soldier had thrown the chair he was touching in the direction of the warrior quite pleased with himself when he heard it connect.

"John!" shouted Teyla.

"Oh no no no!" Rodney kept low to the ground hoping to make less of a mark of himself.

Crouching down, Soldier ran straight towards where the nearest guard had stood. His mark true, as he rammed into the guard; at the same time grabbing the man's arm, holding it high and twisting it. He heard the guard gasp in pain and surprise, the gun going off before falling from his hand. Soldier grabbed blindly for it catching it on the first attempt. He turned in the general direction of the doors and "thought" them locked.

Ronon fired off a shot towards the sound of pain the guard had made and the spark of lights made from the fired bullets; but his shot was slightly too wide and instead took out the other guard who fell to the darkened room's floor with a gasp and a thud.

Soldier smirked at the shouts of the guards outside the door trying to get in. He moved against the farthest wall keeping low, surprisingly quiet as he stepped over and maneuvered around obstacles in his way.

"Sheppard?!" croaked Rodney fright in his voice over not knowing the whereabouts of John.

Teyla had found the light switch but clicking it on and off resulted in no light.

"The lights are not working!" she exclaimed.

"Quiet everyone! Quiet!" hissed Ronon; head turning left and right trying to pick up any noise John made to pinpoint his location.

By then Soldier was where he wanted to be; a large vent he had seen as he had walked around the room; large enough for him to fit in, for him to escape in.

He threw back the vent cover and dived in missing being zapped by the warrior's weapon by inches. Quickly, he pulled himself along trying to get away from the entrance of the vent just in case the hairy mad man decided to dive in after him to shoot him.

The noise of the vent cover being torn from the wall echoed in the dark room.

"The ventilation system!" shouted Rodney. The lights flickered back on at that moment and the locked doors to John's quarters swished open, the guards that had been banging on the door stumbled in guns raised.

Ronon was already hurdling John's bed and crouched in front of the vent's entrance.

John was gone.

He stood and swore in Satedan then turned back to the room and the damage that had taken place in less than 30 seconds. He turned to Teyla and Rodney's stares, to one unconscious guard and the other rolling around on the ground holding his arm and moaning that Sheppard had taken his gun.

One of the guards that had stumbled in kept asking, “Where is he? Where is he?"

Teyla stared at Ronon then Rodney. Col. Sheppard was armed and as dangerous as they knew he was. This was a _big_ mistake.

"I-I can find him." stuttered Rodney pulling out his tablet and heading towards the doors. He pushed past the guards still pointing their guns at no one.

"He's gone, you morons." huffed Rodney as he strode away.

Ronon stormed from the room, his blaster armed and ready.

“I knew this was a bad idea!"

Teyla tapped her comm.

"Mr. Woolsey?"

_“Yes Teyla? How is Col Sheppard?”_

"Col Sheppard…has escaped. He is armed."

_“What the hell happened?”_

“I am sorry sir, we misjudged the situation. We misjudged him."

There was a moment of silence then a sigh dripping in anger and resignation.

_“We have to put the city in lock down. We can't have him running around the way he is.”_

Teyla nodded to herself in agreement.

“Ronon has started searching for the Colonel. I will accompany Rodney and we will search for him as well."

_“I'll start assigning search teams, Woolsey out.”_

Teyla headed towards the lab where she was sure Rodney would be, leaving the two guards to deal with their downed men.

Woolsey was already on the city's communication system stating that a lock down of the city would occur and that no one but military personnel would be allowed in the hallways. On the comm line exclusive to the military personnel, he stated that no one under any circumstances should try to confront the Colonel, but to wait for back up.

ooooo

Meanwhile, in the ventilation system, Soldier blinked rapidly while he continued to quickly make his way forward gripping his newly acquired gun tightly in his hand. He was having some trouble catching his breath and the ventilation shaft seemed to shift and dip in front of him.

He swiped at the sweat on his face then shook himself and continued forward.

**TBC**


	7. Chapter 7

" _Father, where are you? Father….FATHER!"_

Soldier jerked slamming into the side of the vent he was lying in, his breath coming in huge gulps.

It took him a few seconds to remember where he was. He took several large breaths to steady himself while grabbing the gun lying at his side. He must have grayed out for a moment.

He wiped his face with the back of his hand.

_I gotta get outta these vents!_

They would find him too quickly if he stayed where he was.

Pulling himself along, he struggled to maintain his focus. He had some control of this place, the lights and the doors reacted to his will. If he was right, if his hope held true, this city was like the ancient weapons that bent to his will. And if that was so, then he had the largest weapon he ever encountered at his disposal.

ooooo

"There, there he is!" Rodney pointed frantically at a lone dot moving across the screen in front of him.

Rodney tapped his comm. “Lorne?"

_“McKay?”_

“I located the Colonel. He's out of the ventilation system. He's in a hallway east of the tower, one floor down."

_“Got it, Lorne out.”_

Teyla smiled, "Good work, Rodney." then handed him his LSD and they hurried off.

ooooo

"Man, I wish I had my P-90 right now."

"What was that Lieutenant?" whispered Lorne to one of the men on his search team.

"Sorry sir, just wishing I had something a little more powerful to work with then this stunner."

"Remember who we're searching for Lieutenant."

"Oh I remember sir. I'm just not looking forward to facing off with him. Seeing in his condition he'd probably shoot me with, you know… actual bullets before surrendering."

Lorne frowned slightly, continuing on down the hallway they were in. He couldn't reprimand the officer because it would be unfair seeing he was thinking the exact same thing.

ooooo

**Why were they hunting the gene carrier? This was quite wrong. No harm could come to him. Atlantis shook herself. She would protect him.**

Soldier was a shadow, silently moving down the hallway. Raylan had taught him in stealth came victory. He hadn't come upon anyone since leaving the ventilation system.

_No one, there's no one around._

Soldier knew what that meant. Civilians were easy hostages. Get them out of the way. The rest, they were hunting him, and he wasn't about to be easy prey.

Staticky humming flared through his mind and Soldier ground his palm into the side of his head.

"Not now…shut up...shut up!" he groaned.

A soft creak…

Soldier's eyes widened and he burst into a full-on run firing blindly behind him as a stunner blast hit the wall where he was a millisecond ago.

The damned Lanteans had found him!

A voice shouted behind him.

"Colonel Sheppard, STOP!"

He turned and fired down the hallway. Coming to a stairwell he took the stairs up two at a time until he got to the top clearing. Slowly walking backwards he kept his gun aimed at the stairwell.

As he passed a door it slid open and a blast of cold air hit him in the face.

Startled, he turned looking through the open doorway in awe. Stepping through the door his mind momentarily forgetting he was being chased; he found himself on a platform overlooking an ocean, its powerful waves crashing some feet below. Soldier drew back in surprise then stepped to the edge. Turning, he gazed up and around at the magnitude of the cityscape. He couldn't believe how massive it was.

Now he knew…Atlantis was immense.

_They would attack Castima? Why would they need to?_

He heard the door hiss open behind him and in one smooth movement he dropped over the side of the platform; one hand grasping a small stone pillar at its corner. His feet silently, furiously grasping for purchase until they found a tiny ledge.

Soldier barely hanging on waited.

ooooo

"I don't get it, he should be right here! The life signs detector says he's right here!"

"Quiet!"

Soldier breathed deeply and heard one of the voices shout out, "Col. Sheppard? Sir, enough’s enough!"

Soldier saw the shadow of the man first. As the man stepped towards the edge gun raised to peer over, Soldier reached up and grabbed him by the ankle and with a yank pulled the man off the platform.

A scream followed by a splash and Soldier aimed his gun at the edge of the platform just as the other man's head appeared, arm outstretched towards the water. "No!"

The man's eyes widened at the sight of John clinging to the platform with one hand, the other hand holding a gun that was aimed with deadly precision at him.

"Throw the weapon over the side." barked Soldier.

The young man in uniform just stared at him until he saw John raise the gun slightly so that it was now aimed at his head.

"I won't ask again."

The young uniform dropped the stunner over the edge.

Solider wanted to shoot him right then and there, but he didn't know how close the others were and he didn't want to draw their attention. He glared at the man.

"Now jump."

"What?" He was tempted to make a run for it, but the dark way the Colonel was looking at him, he didn't think he'd make even a step before he was cut down.

"Sir, please no!"

He saw John's finger twitch on the trigger.

"Jump!"

Eyes rolling crazily in his head in fear, looking behind him hoping for reinforcements but getting none, the young uniform with a cry leapt of the platform to the waters down below.

Soldier heard the splash, then turned and threw his gun up on the platform then slowly pulled himself up.

He lay there for a moment catching his breath staring up at the sky. Suddenly he was overcome by a feeling that he was flying over the crests of the waves through the blue of the sky. A ripple of pleasure swept through him as he ran his hand through his mist damp hair.

"What the..?" He sat up, confused, then got to his feet grabbing his gun.

_How did they find him?_

He closed his eyes and breathed deeply going back in his mind a few moments to what the men had said.

_I don't get it, he should be right here! The life signs detector says he's right here!_

His eyes flew open. Life signs detector! No wonder they had found him.

Soldier snarled, glancing at the door then at the edge of the platform then back again. Running to the other side of the platform, he spied a small balcony and doorway a few feet across and a few feet below from his location. Gauging the distance and studying the lay of the wall structure he figured he could scale the wall and make it to the balcony. He knew more Lanteans weren't far behind the two now in the water. His weapon was almost depleted; he would need more ammo before he could face them. He would have to find their armory and to find a way to get his captors off his tail.

Soldier was inches to the balcony when he heard the door above and to the left of him hiss open. Seconds later he was climbing over the railing and heading through the doorway, gun raised as he heard in the distance…

" _Oh dear God, they're in the water!"_

ooooo

Ronon made his way to the armory and found a darkened corner in the room. Crouching into a comfortable position, he waited.

**TBC**


	8. Chapter 8

"What do you mean you haven't found him yet?"

"With all due respect Dr. Beckett, the Colonel isn't exactly easy to pin down…especially here in the city."

Lorne paced the infirmary watching as Carson tended to the two lieutenants who were dragged from the water.

Carson pulled the blanket tighter around one of the lieutenants lying shivering on a gurney.

"I know lad, I know." Carson sighed heavily. "The Colonel can be like the wind when he puts his mind to it. I'm just saying that with the serum breaking down in his system and all I'd rather him be here in the infirmary then wandering through the God forsaken bowels of the city. And seeing that he's in the state of mind that he could do this…" he gestured at the shivering lieutenant.

Lorne nodded in understanding. "Take care of my men, I'm going to meet up with Teyla and Rodney. Don't worry Carson, we'll find him."

"Aye lad, just mind he doesn't find you first."

ooooo

Soldier was trying to stave off his frustration but it was building rapidly. The city was way too big. He'd never find the armory!

The floor suddenly tilted in front of him and he quickly held onto the wall to steady himself.

"Dammit! Not now!" he whispered heavily. "Shake it off, Soldier…shake it off! You are..."

" _Father?"_

His eyes widened, a few feet down the hallway he was in stood a little boy dressed in a Castiman tunic, his hair jet black.

" _Father? Where did you go? Why did you leave us?"_

Soldier took a step forward, then noticed he couldn't quite make out the boy's features, they seemed blurred. His hair was matted down…blood dripped from it down the sides of his face.

"I…no, I…”

" _Father, you left us…you left us to die!"_

Soldier cried out jamming his fists into his eyes.

A moment later when he looked up the boy was gone, there was no one in the hallway but himself.

"Enough!" he yelled.

He hit the wall with an open hand and felt his hand rebound back. Surprised, he slowly moved his hand back to the wall and felt the palm of his hand start to tingle and sharp pin pricks run through it. Then he was physically pushed away from the wall by a wave of energy that passed through him. An image washed over him of himself and the warrior who had shot at him, they were eating together at a table and laughing.

_No...impossible!_

Soldier grunted, shaking his head then slowly put one hand on the wall, then the other. The energy he felt was amazing, it was like the walls were breathing. He glanced down the hallway to make sure no one was sneaking up on him then turned back to the wall.

The staticky humming in his head grew louder.

"Okay, I don't know exactly how this works," he said to the wall.

"But I am Soldier and I should have command over you. I controlled the lights and the doors and now I need to control the detectors that the Lanteans have. They must not locate me. I need their detectors to lose track of where I am. I need that right now!"

**_Atlantis stretched and all across the city on the search parties LSDs solitary spots of lights started flicking on their detectors._ **

Soldier felt the energy in the wall grow suddenly and the lights in the hallway flickered.

He would take that as a sign that his command worked, for now anyways.

He bit his lower lip in thought then turned to the wall,

“Show me where the armory is."

Another surge of energy and he heard a small _whoosh_ behind him.

A hidden panel had opened revealing a monitor with what looked like a map of the city. Soldier grinned at the wall then ran over to the monitor. A small red light was blinking in a section of the city he wasn't far from.

_That must be it._

Soldier stance was determined and he slipped off quietly down the hallway.

ooooo

Rodney motioned to the stairwell and whispered to Teyla and Lorne who had recently joined them.

"One floor up, one hallway over."

They both nodded at him and they all moved forward, suddenly the hallway lights flickered. Rodney glanced up at the lights in annoyance then back at his LSD.

"What the hell?" he hissed.

"What is it, Rodney? Teyla whispered.

Rodney frowned, "Life signs, solitary life signs are popping up all over the city."

Teyla and Lorne stared at the LSD in Rodney's hand.

Teyla looked at Lorne, “Do you think Mr. Woolsey has overturned the lock down order without telling us?"

“What, you think those might be civilians in the hallways?"

Teyla nodded.

Lorne tapped his comm.

“Woolsey, this is Major Lorne."

_“Yes Major?”_

"Did you overturn the lock down order?"

_“No, why?”_

"We're picking up multiple solitary life signs throughout the city."

Slight pause

_“No, the lock down is still under effect. Do you think this is the Colonel's doing?”_

"I'd rather hope not, sir."

_“I'll assign one of the search teams to make sure all civilians are in their quarters. For now, just find the closest life sign near you.”_

"Yes sir, Lorne out"

"So…" said Rodney.

"So, we keep looking." sighed Lorne. He looked at the LSD then suddenly grinned.

"Notice anything?"

Teyla and Rodney both looked at the screen.

“There is only one life sign that is moving." stated Teyla.

Rodney smiled. "Ha! He's good, but he isn’t that good! We gotcha, Sheppard!"

Teyla quickly turned down the hallway in the direction of the moving life sign, Lorne and Rodney following. She was trying to dampen her increasing fear that if they didn't find John soon that something horrible was going to happen.

ooooo

Soldier stood outside the doorway to what he was sure was the armory. His eyes and ears focused on the hallway he was in, making sure that he had time to grab what he could before he was found out.

Silence reverberated through the hallway. Soldier took a step forward.

“Father?”

The boy with the blurred face stood in front of him, closer now.

Soldier’s eyes widened for a moment, then he shut them and took a quick breath.

When he opened his eyes the boy was gone.

Anger marched its way across Soldier's face.

He would burn this city to the ground for what they did to him.

He stepped through the doorway into the armory.

_Yes!_

It was just as he imagined, almost like a playground for likes like himself. He touched a few items reverently then finding an empty tote nearby began pushing ammo clips and guns into it.

ooooo

Ronon peered out from where he crouched watching as John bagged the weaponry.

He didn't want to startle Sheppard into blinking out the lights again. He didn't dare fire a weapon in there in the dark. Who knows what he'd hit?

He slowly started to stand when Sheppard suddenly froze, his head jerking in Ronon's direction.

_How did he..?_

Ronon growled rising to his full height, raised his weapon and fired at his friend.

ooooo

Soldier felt the presence before he heard anything and dropped to the ground in one fluid movement as an energy beam slammed against the wall where his head was seconds ago.

He fired blindly over the crate he was hidden behind hoping to end the pestering warrior's life.

Ronon dropped to the floor avoiding the bullets his friend was firing back at him, he never felt so sad and furious at the same time. Crouching, he slowly made his way behind the weapons crates trying to get closer to John.

"I'm not going to allow you to take me again." John said, a hollow echo from the other side of the room.

Ronon kept silent and shuffled closer to the voice.

When they got their Sheppard back he was going to make a trip to Castima and make them regret what they had done to his friend.

He came to the area where he heard Sheppard's voice coming from and dove to the ground firing behind the crate he was sure Sheppard was hiding behind. The energy beam from his weapon slammed into the bare ground.

He whipped his head around at a movement out of the corner of his eye just in time to shield his head as John jumped from his hiding place and was about to bury the butt of his gun in Ronon's skull. Ronon kicked John's legs from out beneath him and then the fight was on.

In the crate filled room there wasn't much space to fight so Ronon and John were equals in their attempt to bring down the other.

With both of their weapons knocked aside, they were locked in hand to hand combat. Ronon was taken aback by the stealth of John's attacks and both got a few stray hits in. Finally he growled and went in for the finish when John crouched so quickly that Ronon missed it and he kicked Ronon hard across the knee. Ronon gasped and breaking his stance bent forward. John took that moment to pull two heavy crates filled with weapons down on him and he collapsed under their weight.

Soldier ran over and grabbed the bag he had been filling, threw in a few more ammo clips and grabbed a few small round metallic objects for good measure and threw them in too. They looked like a weapon he had used from the bunker so he had an idea of what they might do. He made for the door but turned as he saw Ronon slowly pushing aside the crates and rising from the floor. Soldier scowled.

_This guy needed to stay down!_

Ronon cracked his neck and slowly got to his feet, with eyes slightly unfocused he tried keeping his weight off his knee while looking for John and his weapon.

He heard the two sounds at the same time. The door to the armory swished open and John appeared out of nowhere backing out of the room with a smile on his face, fury in his eyes and his gun aimed at Ronon.

It took him a split second to realize the other sound he heard was a metallic clink. He looked to his right as the door swished closed and saw a grenade slowly settling in a large crate filled with other grenades. A second glance and his eyes grew wide.

_No pin! Sheppard!_

Ronon turned and ran for the door just as the grenade went off causing a chain reaction with the other grenades. The crate exploded in a thunderous clap and shards of metal and wood shot across the room. The blast knocked Ronon to the ground as metallic shards embedded themselves into his back along with a long thick shard of wood from the destroyed crate.

His head slammed heavily against the ground and then there was silence and Ronon was still and the blood pooling by his head was startling.

**TBC**


	9. Chapter 9

Rodney was frightened, but he couldn't tell if it was for Sheppard, or for himself.

_Damn it, Sheppard!_

He started going through in his head all the ways that he could wipe the Castimans off the map when he noticed Lorne slowing, one hand by his ear. A moment later Lorne turned to them.

"There's been an explosion in the armory."

Teyla, eyes widening turned and ran towards the armory, Lorne and Rodney rushing to catch up.

Carson and his team had just got there as they arrived and were assessing the situation. Carson knelt next to Ronon and softly tuttered under his breath.

Teyla touched the doctor's shoulder, “Is he..?" she started, afraid of the answer.

Carson glanced up at her and grimaced.

"No love, he's not dead. But we have to be very careful here. You see this piece of wood?"

He pointed to the wood protruding from Ronon's back. "It's quite close to his spine. We have to be extremely careful how we move him." He nodded to the four orderlies standing nearby and they slowly lifted Ronon onto a gurney taking care not to jar him in any way. Carson nodded at them again and they very slowly pushed the gurney forward towards the infirmary.

"Dr. Beckett?" said Teyla.

Carson got to his feet "I canna tell you anything yet. There's definitely a brain injury, I'm hoping nothing more than a concussion and there may be some spinal damage, but I'm hoping not, love." He squeezed Teyla's arm and hurried off. "I'll let you all know as soon as I have more information."

Teyla tightened her jaw in an effort to stave off the tears forming at the corner of her eyes. She turned to Rodney and saw that he was doing the same thing.

Suddenly, she grabbed his arm. "Come, Rodney."

"Wh-where are we going?"

"I know where the Colonel is heading next."

ooooo

Soldier lay on his stomach in a darkened corner of a hallway. He couldn't move…he felt like he was burning from his inner core. Like someone had thrown him into the burning tar pits on Kalthos.

_Help me…God…H-help me…_

He had been moving along fine until his legs gave out from underneath him and he flopped to the ground. He stretched for his gun and bag that had flown out of reach and slowly pulled himself into the nearest darkest corner he could find.

_They would find him now for sure...they would…_

Soldier shed a tear over the shame his dead family would have felt towards him. He couldn't get captured like this…but he could barely hold his head up.

_Please…please…_

He slowly inched his hand to the wall and pressed his palm against it.

"Please help me" he whispered to no one and every one.

ooooo

**Atlantis perked up. The gene carrier was asking for her help. She was not clear on what to do. She could beckon the others to his location. But the others were hunting him and he had no memory of them. She could let no harm come to the gene carrier, but she had a plan.**

Soldier's eyes were slowly rolling in his head when a surge of energy ran from the wall through his arm like a bolt of epinephrine to his system. He gasped, eyes widening and flew to a sitting position grabbing his chest. It felt like a thousand spikes had just shot through his body.

“What the..!”

Soldier felt his hand drawn to the wall again. He closed his eyes when an image shot through his mind of a room with a large chair with symbols in it. Something told him this chair was very powerful and that sitting in it would put him in sync was all the weapons in the whole city. He could destroy his prison in one swoop. Closing his eyes tighter he found that he suddenly saw how to get to the room.

Soldier slowly pulled himself to his feet with a feral grin. He was still so very hot, but he had one more mission to execute, and if he died trying he would know that he did his very best.

ooooo

"Teyla?" Rodney panted as he hurried along next to the diminutive warrior.

“We don't need your LSD Rodney." rushed Teyla, making sure her stunner was in working order. She glanced behind them to see Lorne coming up on their six. He was slowly turning in a circle as he walked keeping aim everywhere.

"I know where the Colonel is going. The chair room"

"How…"

"That is where I would go. He must know he cannot make it through the gate and he has come to realize the power he holds here in the city. I believe that by now he must have been drawn to the power of the chair. He will most likely use it against us, we must hurry!"

Rodney fumbled to put the LSD away then pulled his stunner out, holding it tightly in fear and urgency and followed Teyla, Lorne steadfast behind them.

ooooo

Soldier felt almost like he was in a trance. From corridor to corridor he was left unhindered no Lanteans running him down and then he was there.

He peered around the corner to the hallway to the door to the room with the chair. It was guarded by two men whose eyes flicked from left to right not really guarding. They were so tense that he could have snuck up on them and tapped them on the shoulder and they would have collapsed where they stood.

Soldier's eyes narrowed and quietly he sifted through his bag and smiled as he pulled out one of the pin bombs he had used on the crazed warrior.

_A very sufficient distraction._

He pulled the pin on the bomb and when the guards' eyes shifted he rolled it down the hallway past them. He smiled as he saw the inept guards do exactly what he thought they would. They ran away from the bomb down the hallway straight to him. As the first guard ran past, Soldier tackled him grabbing his weapon arm and spinning him in front just as the other guard shot at him. The guard he had tackled jerked and slumped not before Soldier used the downed guard's own stunner and shot the other guard right in the face.

Soldier's deadly gaze landed on the door to the room. He threw the guard's stunner to the ground then checked his gun cocking it then made his way to the door. He could feel the energy thrumming through him.

_This is REAL power._

He stepped through the door gun raised, and the door quietly slid shut behind him.

ooooo

Carson took a deep breath and one of his nurses pulled his surgical mask on. He stood surrounded by six of his medical staff, all consummate professionals. In the center of the circle on a gurney lay Ronon. Carson tried not to think what would happen if he lost Ronon on the table, what would happen to John's team, hell, what would happen to everyone who came to love this silent loyal warrior over the time he's been with them.

He took another deep breath, squeezed his hands into fists then shook them loose. He looked at his team, eyes steady.

"Let's begin."

ooooo

Teyla, Rodney and Lorne crouched near the end of the corridor where John had been a few minutes before. Lorne checked on his downed men and nodded. They'd be okay. They eyed the damage the grenade had done then moved slowly towards the door to the chair room; Lorne on one side, Teyla and Rodney on the other.

Teyla waved her hand over the door opener. Nothing, John had locked himself in.

ooooo

Soldier scanned the room with his gun, when he saw he was alone he lowered the gun and mind locked the doorway; then made his way to the center of the room where the chair he saw in his mind stood.

He slowly slid his hand across it reverently. The power coming from this chair, he was at a loss of words. If he could get this chair to Castima and show Raylan.

Suddenly he felt the need to sit in the chair, and almost against his will he felt himself drawn to the chair and up and onto it. Automatically the chair lit up brilliantly and the back moved downwards so Soldier was almost in a lounging position. This shocked him and he tried to sit up but he found he couldn't. He convulsed as he felt himself being invaded by a power he was sure would split him in half.

Then...then he saw _everything._

He was a part of everything. The city became like a vapor invading every pore of his body. It was too much...

_Too much!_

Then all of a sudden he saw them, the drones. There were hundreds of them laying there…waiting for his bidding. Soldier grinned and let go, allowing himself to fully be part of the power racing through him. He pushed his mind towards the drones and began to power them up.

_Straight up, then straight down…blow this city to kingdom come._ He commanded them.

ooooo

Woolsey was on the comm with one of the search teams when Chuck raced into his office.

"Sir! Sir!"

"Woolsey out."

He stood up from his desk “Chuck, what is it?”

"The drones, they're firing up."

"What!" Woolsey came from around his desk and followed Chuck out to the gate room and monitors.

"How many of them?"

"All of them, sir!"

Woolsey's heart stopped, his eyes widening "Who's doing this?"

Chuck typed furiously at his keyboard then gulped heavily pushing away from his station. "It must be Colonel Sheppard sir, the chair room is in use."

Woolsey rubbed his brow. "Where…where is he aiming them at?"

Chuck turned back to his keyboard and typed some more.

"Oh no..."

"What is it?"

"He's aimed all of them straight up."

Woolsey frowned "Into the atmosphere?"

Chuck turned to his superior "Straight up sir, just far enough to turn around and come back down…armed. He's going to blow the city."

Woolsey tapped his comm. "Major Lorne!"

Lorne jerked at the urgency of Woolsey's voice in his ear.

_“Sir!”_

"The Colonel has activated all the drones. He's going to turn them on the city. He's in the Chair room!"

_“Yes sir, Teyla, Rodney and I are right outside the room. He's locked us out.”_

"Well you better find a way in. NOW!"

_“Yes sir, Lorne out!”_

Lorne rushed the door and tried to force it open.

ooooo

**Atlantis had enough. She would not stand by and be destroyed. Not even by the gene-carrier. She grasped his mind and opened it wide.**

Rodney was about to yell at Lorne that he wasn't Superman and couldn't possibly pry the door open when a scream came from the other side of the door; they all froze. The scream came again like the sound of wounded animal caught in a bear trap, shattering their hearts.

Teyla was first to move. She ran to the door and pounded at it.

"Colonel Sheppard! John!"

Soldier was caught in an avalanche of memories. He struggled to get out of the chair but he couldn't move, not at all. He felt like he was drowning in lava as someone split his head open again and again with an axe.

Outside the door, Lorne's comm rang.

"Lorne." he huffed, emotion over his friend's screams smothering him.

_“It's Woolsey. You did it. The drones have powered down. You have the Colonel?”_

"No sir…no. He’s…still locked in the Chair room. We can't get in. Something's wrong. He's...he's screaming, sir."

_“Carson is in surgery with Ronon…I'll get someone down there right away.”_ said Woolsey.

"With a blow torch, sir." whispered Lorne.

_“Yes, of course. Woolsey out.”_

Lorne turned to the door, turned to Teyla still banging away and Rodney, eyes wide with his tablet in hand as he tried to find a way to unlock the door.

ooooo

He was chained to a table and they were electrocuting him!

_Why were they electrocuting him?_

He looked around the table and saw the warrior, the woman and the scientist laughing at him as they kept spinning the dial.

"Stop! STOP IT!" Then suddenly it was Raylan by the table and _he_ was doing the torturing.

Teyla stopped banging on the door "John?"

"Stop hurting me! I want to go home…I want to see my family!"

Soldier turned his head slightly and saw a woman and boy standing near the chair, the same boy as before. They were both covered in blood, their faces were blurry and warped like in some madman's nightmare.

“ _Where were you? You left us to DIE!"_ Their harsh words stabbed through his mind like shards of glass.

"Noo!!"

Outside the door Rodney stepped back and stared at Lorne in a panic. Lorne pushed Teyla and Rodney aside and opened fire on the door crystals, hoping to short out the lock mechanism and save his friend.

ooooo

**The gene-carrier's mind was a mess. Atlantis strained and pushed and pulled to put all the memories back in the right order. She needed to save him, his people outside could only hinder this moment so she allowed the door to remain closed. She did not want to kill the gene-carrier but his mind was so tired and she had to pull so deep.**

Soldier jerked in the chair as the lights flickered in the room and the outside hallway. Flickers of memories like a movie on fast forward flew through his mind.

The warrior and him laughing together, fighting side by side. The woman handing him a cooing baby, the scientist and him racing mechanical cars together…

But then they were torturing him, drowning him, leaving him so cold and so alone as he cried out for Raylan, Raylan his friend who would…

An image of Raylan hit him, he was laughing at him as Soldier crawled on a dirt ground screaming in agony!

Then the images came faster and faster. He was standing in front of large house not on Kalthos or Atlantis and a man was yelling at him. Then he was surrounded by sand and the noise was deafening. Then monsters with teeth in their hands were leaning over him sucking the life from him. Then the Castimans saved him, no, the Lanteans…no...he was Soldier…he was...oh god...he couldn't breathe…he couldn't…the memories flew through his mind too fast now. No..no…

"STOP!"

He was plunged into a bright light and felt his mind and body expand to the point of breaking, then suddenly everything contracted…

And all the lights in the city as one exploded.

Then there was silence.

**TBC**


	10. Chapter 10

Carson slowly leaned back from over Ronon's body. He had shielded the Satedan’s head and open surgical wound when all hell exploded and the lights blew out.

"…bloody hell was that?" he whispered.

He couldn't see Ronon in the abrupt darkness, but the heart monitor beat quietly, steadily.

Thank God they had gotten the shard of wood out before he had thrown himself over Ronon, the damage he could have done.

Carson breathed a stuttered heavy sigh borne of fear and relief then shook himself. "Come on now." he whispered to his staff who he could sense standing around him frozen in the darkness. "Torches, get us some torches."

"Torches, sir?" he heard someone say.

"Flashlights ye bugger! Hurry now, we have a patient to save."

ooooo

One by one their flashlights permeated the darkness, first Lorne's then Teyla's then Rodney's.

"Are you guys okay?" whispered Lorne brushing shattered glass from his hair.

"Yes." whispered Teyla "I am well." She brushed glass from her shoulders.

Lorne turned his flashlight on Rodney who blinked wide eyed and nodded.

They all turned as the door to the Chair room slid open. Lorne stepped through the doorway first followed by Teyla then Rodney. Inky darkness cloaked the room permeated sporadically by their roaming flashlights. Subconsciously, they all slightly crouched when their flashlights turned to the chair to find it empty.

Teyla took a step forward wincing at the noise as her foot crunched on the shattered glass from the overhead lights and looked down at her feet in annoyance, when she looked back up she gasped as her flashlight caught sight of John hunched in a corner of the room his eyes wide and dangerous. His gun gripped in his shaking hand.

She swung her stunner up at the same time he aimed his gun at her.

Astonished, she fired her weapon and so did he.

She missed.

He didn't.

ooooo

As soon as the bullet left his gun it was like a curtain fell away and John stood there eyes wide in confusion.

_What was happening?_ He felt the gun in his hand but couldn't see it.

He was in darkness, there were people in there with him…flashlights like strobes permeating the inkiness. Soon the flashlights turned to the ground a few feet from where he stood.

His heart thudded to a stop, frozen solid in horror as he took a shaky step forward.

_Who was...who_ …

"Teyla?" he whispered.

The beam from the flashlights turned towards him blinding him. He held one hand to his face blocking them.

_Did he do that? Did he shoot Teyla?_

_Did he shoot Teyla!?_

The last thing he saw was a blast of light shooting at him through the darkness, then nothing.

ooooo

John was on fire. He felt like a thousand hot coals had been tossed on top of him to render him to ash. He tried to scream, to escape, his lungs recoiling against the effort.

Rodney started as John jerked on the bed and moaned. A nurse silently came to the bedside checking John's vitals then hurried away.

Sighing heavily, Rodney turned to his friend. John was tethered to the bed by multiple restraints. They couldn't let him escape again, but Rodney couldn't see that happening. John's temperature had roared to a frightful 105 degrees and he had struck out at anyone who came near him, screaming…begging them to stop torturing him, begging them to let him see his team. Ergo, the restraints donned sadly by Carson and the three orderlies it took to hold John down. Carson had told him that it was John's body fighting the withdrawal of the serum and God knows most likely a side effect to what happened to him in the chair room.

To Rodney it felt almost like it was John punishing himself.

He shook his head sadly.

John had shot Teyla.

He shot...Teyla.

Pulling the privacy curtain aside, Rodney looked at the adjacent bed. Teyla lay there unconscious, but thank heavens alive. The bullet had passed right through her missing any vital organs. She would make it.

But would their team? Ronon was recuperating, he had a severe concussion and had nearly been paralyzed because of the blast, but Carson said that he would most likely make a full recovery.

When told about Teyla, Ronon stopped talking to everyone, even Rodney. Would he forgive John? Would Teyla ever forgive John for shooting her? Would John forgive himself?

Rodney turned back to John's bed side. His temperature was down a little at 102, but it looked like he was suffering horribly.

John moaned again, twisting against the restraints that held him fast.

Rodney covering his mouth with his hand turned and strode from the room.

ooooo

_Let me go, let me go!_

A blurry face leaned over him laughing as he was electrocuted again and again.

_What is your name? WHAT IS YOUR NAME?_

"I'm Lt. Col. John Sh-Sheppard! I'm John...I'm John!"

Carson stood by John's bed wiping his brow with a cool cloth. Frowning sadly, he watched as his friend feebly tried to free himself of his restraints while screaming his own name.

"Aye my friend, you are."

ooooo

Two months had passed. Ronon had gone with Teyla to the mainland to recuperate. He had been relegated to a wheelchair on Carson's say so and couldn't bear being in the city. Teyla had told Rodney she felt the need to be around her people, to be with her son. Neither had asked about John.

Rodney stood outside John's door. He had barely left his quarters since being discharged from the infirmary. Rodney knocked.

No answer.

"Sheppard, I know you're in there, unless you want me camped out on your doorstep open up."

The door swished open to Sheppard standing grim faced and hollow-eyed, looking like he hadn't slept in days, a gun held down by his side.

"What do you want, McKay?"

"I," Rodney stared at the gun by his friend's side. They had confiscated all his weapons so he wasn't sure where John got it from.

"Rodney…”

"I was wondering if you were hungry and…"

"No." muttered John turning his back and walking towards his bed.

Rodney stepped into John's quarters. "…and…I was thinking maybe we could go to the mess hall. You know...grab a bite."

"I said no, Rodney." John sat on the edge of his bed and stared at the gun in his hand.

Rodney rubbed the back of his neck and sighed. He walked over to the corner of the room and absentmindedly caressed one of the golf clubs jutting out from the golf bag resting there.

"You thinking about taking up golf, McKay?" whispered John still staring at his gun.

"What? No…no."

He sat down next to John and pulled out two power bars from his jacket pocket. He put one on John's lap as he tore open the other one and munched quietly.

He could see it in his friend’s demeanor. John felt that he had failed his team. Rodney knew what that sort of thinking could do to someone like John.

"Sheppard, they finally caught the monster that did this to you. They brought him back, he's in one of the holding cells."

John’s team had been put on indefinite leave until everyone had time to heal over the terrible events that had occurred.

Rodney took some of that time to try to explain to John what had happened. He was the only one that John would even look at or speak to.

The trust issues John struggled with were taking a toll on him. He knew he belonged in Atlantis, but he had also known he had belonged on Castima. He couldn't help but miss the family he never had; this confused and saddened him. Rodney had told him that he had been held underground in a bunker much like the one the ancient weapons they had been found had been hidden in; protected by their sensors by the type of metal that encased it. The search teams had come upon it by a ground search on foot miles from the city walls.

John could recall sporadically what had happened to him. Events like flashes of light blinking on and off in his mind. Everything else, every feeling in between ever second of his nightmares left him feeling dead inside.

He had tried to kill his teammates.

That fact consumed him.

Rodney got up and stood in front of John. "Did you hear me Sheppard? The guy who did this to you is here! John!"

John shook himself out of his reverie realizing what Rodney had said, a sudden blaze of anger rushing through him. Rodney quickly stepped aside as John got to his feet; the sudden rage in his eyes making him get out of the man's way.

His eyes widened as he heard John cock his gun, then he quickly followed him as he strode out the room towards the waiting cells.

ooooo

The door swished open and the guards spun in surprise as John strode into the room, gun raised.

They raised their guns in accord, looking hesitantly at each other.

"Col Sheppard, sir, put the weapon down!"

John's gaze was only towards the holding cell where Raylan Emitan stood looking quite small and stoic at the same time.

"You did this to me?" yelled Raylan when he saw John. He moved to the edge of the cell.

"Soldier! Lower your weapon and let me out of here at once!"

John stumbled as if he walked into an invisible wall.

"Sheppard?" Rodney asked.

"I said lower your weapon, Soldier!"

Rodney watched John's arm waver and start to lower.

John was somewhere else, he was in a darkened room and all hell was upon him.

"Sheppard…John!" hissed Rodney.

John turned to him, his eyes full of frustration and sadness.

Rodney slowly pulled the gun from John's hand and grabbed onto his friend's shoulders.

"You are John Sheppard." He stated then motioned towards the cell. "He didn't win John. He didn't win."

John slowly nodded; Rodney's words seeping into him. He turned to the cell and to Raylan's indignant stare.

"I am…" he pointed his finger and stabbed it towards Raylan.

"I am Lieutenant Colonel John Sheppard. You lose."

Raylan's stare faltered. John's eyes flashed and he turned to the guards.

"Take everything you found in their storage facility. As for this man, the Athosians will know what to do with him."

The guards, who had lowered their weapons nodded in agreement. It looked like their leader was on his way back.

John turned to leave his heart heaving.

_The Athosians…Teyla…_

Rodney grabbed his arm to steady him. "I gotcha, John. I gotcha."

ooooo

_A week later_

After a week of words and tears and soul wrenching screams in the night that Rodney (who had pulled a cot into John's room and wouldn't _"get the hell out or else"_ ) had been witness to and John knew would go to his grave before he'd tell another single soul; they sat at a table with Lorne in John's quarters playing cards.

Laughter echoed through the room. John was still an echo of himself, but he had finally started to open up and had looked Lorne in the eyes as Lorne told him that no one blamed him for what had happened. That it wasn't his fault and the men under him were looking forward to whenever he was ready to lead them again.

John had smiled at that. Sadness still drenched in his eyes.

ooooo

_A few days later_

John opened another beer as he stared out over the sunset lit ocean.

Sighing heavily he took a swig, his feet dangling off the pier.

He looked at his hands. They had the blood of innocent people on them. He didn't know how he could live with that, what he could ever do to make up for what he had done.

He needed his team back. They gave him something to believe in, the strength to carry on when he had nothing left in him to give. John heard a subtle cough behind him and smiled.

_Good ole Rodney._

Rodney sat next to him "This seat taken?"

He smiled and handed Rodney a beer. "Nope."

They sat quietly for a while watching as the sun slowly set behind the waves.

"Uh... McKay?" said John still looking out on the water.

"Yeah?"

He turned to the most aggravating, strongest best friend a man could ever ask for.

"Thanks."

"Thanks?" Rodney put his beer down and pulled out a power bar and started munching on it. 'For what?"

John glanced at him and saw Rodney giving him a side glance while trying to hide his smile behind his chewing.

John laughed and patted him on the shoulder. They sat in a comfortable silence until the sun completely set below the horizon.

"Come on," said Rodney getting to his feet and brushing power bar crumbs off his shirt.

“What?"

"Come on, I want to show you something!"

John exhaled taking one more swig of his beer, draining it then got to his feet following Rodney up the pier.

"Where we goin', Rodney?"

"Patience, Sheppard.” chuckled Rodney from up ahead.

John grinned and followed his friend back to the city.

ooooo

John and Rodney stood in the corridor outside John's quarters.

"You wanted to show me my quarters?"

Rodney rolled his eyes. "You could be so dense...go inside."

John smirked and entered his quarters stopping just inside the doorway at the sight that greeted him.

"Hello, John." said Teyla holding a giggling chubby Torren.

Ronon stood next to her leaning slightly with a cane but looking like the fierce mountain of a man John remembered his friend to be.

"Hey buddy." he grinned at John.

John just stood there, his mouth open, eyes blinking rapidly; his heart swelling then stuttering in his chest.

"John?" Teyla took a step toward him and John took a step back bumping into Rodney.

Torren reached for John, giggling, with wiggly arms and then John broke, covering his face with his hand.

"What I did to you! I’m so sorry!”

Rodney maneuvered John to his bed and sat him down on the edge.

"John…John." whispered Teyla sitting next to him. "It is okay. We are all right."

She looked at Ronon who had pulled up a chair from the table and sat down gently in front of the bed. He smiled at Rodney who sat on the other side of John, then at John.

"Sheppard. It's okay."

Teyla touched John slightly on the shoulder and he glanced at her through tear filled eyes.

"John, we…we had to come to terms with what had happened. I-I felt the need to be with Torren. I wanted him to see me, to see that I was still here. I needed to feel I was still here."

"And I couldn't be here, Sheppard." Ronon's deep timbered voice caused John to turn to him. “I just…I was in no shape the way I was...and after what happened…I needed some time."

"But, you're both okay? You’re okay?" whispered John his eyes glancing from Teyla to Ronon then to his own lap.

"Yes John we are okay, still healing in here..." She placed her hand on her chest and nodded at Ronon who nodded back in agreement. "But we are okay." She placed her hand over John's heart. "We need you to heal too, John."

"I…I thought I'd never see you guys again. The things I did, I…"

"John," Teyla interrupted him. "The things that were done to you! You are a good man. We are sorry we left you how we did. We are a team. We belong together and if you give us a chance we will prove it once again."

John looked at her, astonished. "If I give _you_ a chance? What I did to you both…I…”

"Yeah" smiled Ronon, "But we figured that the John Sheppard we know deserves a second chance."

"Yes," said Teyla. ”And he has earned something even more."

John looked at her expectantly.

"Our forgiveness."

John stared at Teyla, Ronon and Rodney.

_His team. He had his team back._

He felt his heart soar released from the heaviness that had locked him in for so long. With their help he could make things right, he could make up for what he had done.

He was Lt. Col John Sheppard and with his team beside him he could fly.

The overwhelming emotion he felt put him at a loss for words.

But he couldn't help but laugh out loud when Teyla placed the bubbling Torren in his lap and Torren thumped him on his chest with his chubby fist, hiccupped then giggled wildly.

And if someone looked into John's quarters at that moment, they would see a group of people shattered through circumstance but laughing as broken hearts started to heal through the power of friendship.

**The End.**

**Thanks for reading, hope you liked it!**


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